Cell polarity is essential for generating diverse cell functions. The underlying mechanisms of how a cell establishes, maintains, and changes its polarity are poorly understood. Recently, sterol-rich membrane microdomains are found to be associated with these processes. However, both its exact characteristics and importance are still unclear. Here we show microdomains change dynamically in developing and germinating rice pollen with selective enrichment in the aperture and the tip of newly born pollen tubes by use of the sterol-specific probe filipin. Using the sterol extraction sensitivities of microdomain proteins and quantitative proteomics, we identified 237 microdomain-associated proteins from 934 identified pollen detergent resistant membrane proteins. This proteome includes almost all of the known key regulators comprising the polar growth network, and it shows more similarity to front–back polarized HeLa cells than nonpolarized Arabidopsis suspension cells. We immunolocalize flotilin-like protein, a representative of these sterol-dependent proteins and directly visualize microdomains in pollen. These results indicate the presence of microdomains in pollen and pre-established cell polarity around the aperture during pollen maturation. Our findings reveal an atlas of the microdomain-associated proteome in pollen. This work provides useful resources and knowledge needed to further dissect the mechanisms for the establishment and maintenance of cell polarity.